Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014916.1 Corchorus olitorius cultivar O-4 contig14949, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 42843
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:9352 original size:19 final size:20

Alignment explanation


    Indices: 9326--9383  Score: 64
    Period size: 19  Copynumber: 2.9  Consensus size: 20

       9316 CTGTTTGGTA

                                
       9326 ACTGTACAGATGAGATTA-C
          1 ACTGTACAGATGAGATTAGC

             *      *  *        *
       9345 ATTGTACACATTAGATTATGT
          1 ACTGTACAGATGAGATTA-GC

                              
       9366 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       9384 TTAGAACATC


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  19   15  0.50
  21   15  0.50

ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAGC

Found at i:19146 original size:6 final size:6

Alignment explanation


    Indices: 19135--19164  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      19125 TGATTAACCC

                                              
      19135 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA

      19165 CAAAACCATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:42598 original size:110 final size:109

Alignment explanation


    Indices: 42475--42677  Score: 298
    Period size: 109  Copynumber: 1.9  Consensus size: 109

      42465 TATCATGTGC

                          *   *            *   *                           * 
      42475 AAAGAAAAATTATTGAAGTTATAATCTCACTTAGGGACGGATCTTGATATATAAGTTTGATGGGC
          1 AAAGAAAAATTATTAAAGCTATAATCTCAC-CAGGAACGGATCTTGATATATAAGTTTGATGGAC

                              *                          
      42540 AATATAAATTACCTTATGTAAAATTAATCATATCACATCATATAT
         65 AATATAAATTACCTTATGCAAAATTAATCATATCACATCATATAT

                 *              *    *          *                            
      42585 AAAGAGAAATTATTAAAGCTCTAATTTCACCAGGAATGGATCTTGATATATAAGTTTGATGGACA
          1 AAAGAAAAATTATTAAAGCTATAATCTCACCAGGAACGGATCTTGATATATAAGTTTGATGGACA

            *                           
      42650 TTATAAATTACCTTATGCAAAATTAATC
         66 ATATAAATTACCTTATGCAAAATTAATC

      42678 CAAGTAAACT


Statistics
Matches: 82,  Mismatches: 11, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
 109   57  0.70
 110   25  0.30

ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34


Consensus pattern (109 bp):   
AAAGAAAAATTATTAAAGCTATAATCTCACCAGGAACGGATCTTGATATATAAGTTTGATGGACA
ATATAAATTACCTTATGCAAAATTAATCATATCACATCATATAT
Done.